1
|
Velasquez JD, Echeverría J, Guerra CF, Alvarez S. Azido-mediated intermolecular interactions of transition metal complexes. Phys Chem Chem Phys 2024; 26:6683-6695. [PMID: 38321825 DOI: 10.1039/d3cp05798d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The coordinated azido ligand has a variety of ways to establish intermolecular contacts whose nature is computationally analysed in this work on dimers of the [N3-Hg(CF3)] complex with different interactions involving only N⋯N contacts, or with an additional Hg⋯N contact. The applied tools include the molecular electrostatic map of the monomer, an energy decomposition analysis (EDA), a topological AIM analysis of the electron density and the study of NCI (non-covalent interactions) isosurfaces. The interactions between two azido ligands are found to be weakly stabilizing (by 0.2 to 2.7 kcal mol-1), topology-dependent and require dispersion forces to complement orbital and electrostatic stabilization. Those interactions are supplemented by the formation of simultaneous Hg⋯N secondary interactions by about -1 kcal mol-1, and by the ability of the monomer to simultaneously interact with several neighbours in the crystal structure.
Collapse
Affiliation(s)
- Juan D Velasquez
- Instituto de Síntesis Química y Catálisis Homogénea, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain.
| | - Jorge Echeverría
- Instituto de Síntesis Química y Catálisis Homogénea, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain.
| | - Célia Fonseca Guerra
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Santiago Alvarez
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTC-UB), Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain.
| |
Collapse
|
2
|
Ismail TM, Patkar D, Sajith PK, Deshmukh MM. Interplay of Hydrogen, Pnicogen, and Chalcogen Bonding in X(H 2O) n=1-5 (X = NO, NO +, and NO -) Complexes: Energetics Insights via a Molecular Tailoring Approach. J Phys Chem A 2023. [PMID: 38029408 DOI: 10.1021/acs.jpca.3c04181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Nitric oxide (NO) and its redox congeners (NO+ and NO-), designated as X, play vital roles in various atmospheric and biological events. Understanding the interaction between X and water is inevitable to explain the different reactions that occur during these events. The present study is a unified attempt to explore the noncovalent interactions in microhydrated networks of X using the MP2/aug-cc-pVTZ//MP2/6-311++G(d,p) level of theory. The interactions between X and water have been probed by the molecular electrostatic potential (MESP) by exploiting the features of the most positive (Vmax) and most negative potential (Vmin) sites. The individual energy and cooperativity contributions of various types of noncovalent interactions present in X(H2O)n=1-5 complexes are estimated with the help of a molecular tailoring-based approach (MTA-based). The MTA-based analysis reveals that among various possible interactions in NO(H2O)n complexes, the water···water hydrogen bonds (HBs) are the strongest. Neutral NO can form hydrogen and pnicogen bonds (PBs) with water depending on the orientation; however, such HBs and PBs are the weakest. On the other hand, in the NO+(H2O)n complexes, the NO+···water interactions that occur through PBs are the strongest; the next one is the chalcogen bonding (CB), and the water···water HBs are the weakest. In the case of the NO-(H2O)n complexes, the HB interactions via both N and O atoms of NO- and water molecules are the strongest ones. The strength of water···water HB interactions is also seen to increase with the increase in the number of water molecules in NO-(H2O)n. The present study exemplifies the applicability of MTA-based calculations for quantifying various types of individual noncovalent interactions and their interplay in microhydrated networks of NO and its related ions.
Collapse
Affiliation(s)
- Thufail M Ismail
- Department of Chemistry, Farook College, Kozhikode, Kerala 673632, India
| | - Deepak Patkar
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
| | - Pookkottu K Sajith
- Department of Chemistry, Farook College, Kozhikode, Kerala 673632, India
| | - Milind M Deshmukh
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
| |
Collapse
|
3
|
Scheiner S. Adjusting the balance between hydrogen and chalcogen bonds. Phys Chem Chem Phys 2022; 24:28944-28955. [PMID: 36416473 DOI: 10.1039/d2cp04591e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A complex is assembled which pairs a carboxyl group of X1COOH with a 1,2,5-chalcogenadiazole ring containing substituents on its C atoms. The OH of the carboxyl group donates a proton to a N atom of the ring to form a OH⋯N H-bond (HB), while its carbonyl O engages in a Y⋯O chalcogen bond (ChB) with the ring in which Y = S, Se, Te. The ChB is strengthened by enlarging the size of the Y atom from S to Se to Te. Placement of an electron-withdrawing group (EWG) X1 on the acid strengthens the HB while weakening the ChB; the reverse occurs when EWGs are placed on the ring. By selection of the proper substituents on the two units, it is possible to achieve a near perfect balance between the strengths of these two bonds. These bond strengths are also reflected in the NMR spectroscopic properties of the chemical shielding of the various atoms and the coupling between the nuclei directly involved in each bond.
Collapse
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
| |
Collapse
|
4
|
Che J, Pan F, Chen X, Zhang Y, Tao N, Fu Y. Screening of Oxygenated Aromatic Compounds for Potential Antifungal Activity against Geotrichum citri-aurantii through Structure-Activity Relationship Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13787-13795. [PMID: 36240172 DOI: 10.1021/acs.jafc.2c04955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Sour rot caused by Geotrichum citri-aurantii (G. citri-aurantii) is responsible for huge economic losses during citrus fruit storage. However, the availability of chemical fungicides for controlling this disease is rather limited. In the present study, the antifungal activities of 25 oxygenated aromatic compounds against the mycelial growth of G. citri-aurantii were determined, and their corresponding structure-activity relationships were illustrated. Salicylaldehyde (pMIC = 2.689) possessed the strongest inhibitory effect on G. citri-aurantii growth, followed by thymol (pMIC = 2.478) and o-phthalaldehyde (pMIC = 2.429). Molecular electrostatic potential and molecular orbital analysis showed that the antifungal efficiency of test compounds was determined by the number and location of hydroxyl and aldehyde groups and the length of the ester chain. All compounds were selected for quantitative structure-antifungal activity relationship (QSAR) analysis. A three-dimensional-QSAR model of G. citri-aurantii inhibitors was established and demonstrated good predictive capability [comparative molecular field analysis, q2 = 0.532, optimum number of components (ONC) =10, R2 = 0.996, F = 560.325, standard error of estimation (SEE) = 0.034, and two descriptors; comparative similarity index analysis, q2 = 0.675, ONC = 6, R2 = 0.989, F = 263.354, SEE = 0.054, and five descriptors]. QSAR analysis showed that substitution at position 1 with hydrophilic and electron-withdrawing groups produced a hydrogen donor and thus improved the antifungal activity. In contrast, substitution at positions 4 or 5 with hydrophilic and electron-donating groups decreased its antifungal activity. These findings can provide theoretical guidance for preparing effective antifungal drugs for controlling sour rot in citrus.
Collapse
Affiliation(s)
- Jinxin Che
- School of Chemical Engineering, Xiangtan University, Xiangtan411105, P.R. China
| | - Fei Pan
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing100093, P.R. China
| | - Xiumei Chen
- School of Chemical Engineering, Xiangtan University, Xiangtan411105, P.R. China
- Postdoctoral Station of Chemical Engineering and Technology, Xiangtan University, Xiangtan, 411105Hunan, P.R. China
| | - Yonghua Zhang
- School of Chemical Engineering, Xiangtan University, Xiangtan411105, P.R. China
| | - Nengguo Tao
- School of Chemical Engineering, Xiangtan University, Xiangtan411105, P.R. China
| | - Yishan Fu
- Faculty of Agriculture and Food, Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming, 650500Yunnan, China
| |
Collapse
|
5
|
Scheiner S. Properties and Stabilities of Cyclic and Open Chains of Halogen Bonds. J Phys Chem A 2022; 126:6443-6455. [PMID: 36084144 DOI: 10.1021/acs.jpca.2c04967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Open and cyclic chains from two to eight units of ICl and IF are constructed and examined by density functional theory (DFT) calculations. These chains contain either I···I or I···X halogen bonds (XBs) where X refers to Cl or F. The closed rings are more stable than the open chains due to the presence of an additional XB and enhanced cooperativity. This pattern is true even for most trimers where there is sizable geometric distortion in the rings. I···F rings are generally more stable than the corresponding I···I cycles as the I···F bond is stronger than I···I even in the simple dimer. However, I···I rings are comparable in energy to I···Cl. It is possible to construct I···I rings of at least as large as eight units, which are held together exclusively by XBs. On the other hand, the maximum possible size of I···X rings is 6. Red shifts are observed in the I-X stretching frequency bands, which magnify as the chain, both cyclic and open, grows longer. The NMR chemical shielding of the I atoms increases for I···I chains but diminishes when I···Cl bonds are present.
Collapse
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| |
Collapse
|
6
|
Chandra S, Mahapatra N, Ramanathan N, Sundararajan K. Unique O═N...O Pnicogen Interactions in Nitromethane Dimers: Evidence Using Matrix Isolation Infrared Spectroscopy and Computational Methodology. J Phys Chem A 2022; 126:3511-3520. [PMID: 35608948 DOI: 10.1021/acs.jpca.2c02248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Geometries of nitromethane homodimers have been revisited using ab initio and density functional methodologies, following their formation within cryogenic matrices, confirmed using infrared spectroscopy. In contrast to the claim that the intermolecular interactions are due to dispersion forces or very weak hydrogen bonds, in the present work, concrete evidence for the prevalence of O═N...O pnicogen bonding has been presented. The pnicogen bonds have been found to be primarily responsible for the characteristic geometry of a homodimer. The formation of a nitromethane dimer with pnicogen bonding stabilization is evidenced using matrix isolation infrared spectroscopy with Ne and Ar matrices and computations. The interactions within homodimers have been characterized using quantum theory of atoms in molecules, natural bond orbital, energy decomposition, electrostatic potential mapping, and noncovalent interaction analyses. The larger intermolecular separations in liquid nitromethane indicated by previous molecular dynamics-based studies alongside the supposed invariance of infrared spectra in the gas phase and liquid phase could have led to the assumption of a lack of intermolecular interactions. However, the prevalence of hydrogen and pnicogen bonds across these larger than usual separations is affirmed by the geometries presented here.
Collapse
Affiliation(s)
- Swaroop Chandra
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, Tamilnadu, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Nandalal Mahapatra
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, Tamilnadu, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Nagarajan Ramanathan
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, Tamilnadu, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Kalyanasundaram Sundararajan
- Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, Tamilnadu, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| |
Collapse
|
7
|
Ibrahim MAA, Moussa NAM, Saad SMA, Ahmed MN, Shawky AM, Soliman MES, Mekhemer GAH, Rady ASSM. σ-Hole and LP-Hole Interactions of Pnicogen···Pnicogen Homodimers under the External Electric Field Effect: A Quantum Mechanical Study. ACS OMEGA 2022; 7:11264-11275. [PMID: 35415328 PMCID: PMC8992284 DOI: 10.1021/acsomega.2c00176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
σ-Hole and lone-pair (lp)-hole interactions within σ-hole···σ-hole, σ-hole···lp-hole, and lp-hole···lp-hole configurations were comparatively investigated on the pnicogen···pnicogen homodimers (PCl3)2, for the first time, under field-free conditions and the influence of the external electric field (EEF). The electrostatic potential calculations emphasized the impressive versatility of the examined PCl3 monomers to participate in σ-hole and lp-hole pnicogen interactions. Crucially, the sizes of σ-hole and lp-hole were enlarged under the influence of the positively directed EEF and decreased in the case of reverse direction. Interestingly, the energetic quantities unveiled more favorability of the σ-hole···lp-hole configuration of the pnicogen···pnicogen homodimers, with significant negative interaction energies, than σ-hole···σ-hole and lp-hole···lp-hole configurations. Quantum theory of atoms in molecules and noncovalent interaction index analyses were adopted to elucidate the nature and origin of the considered interactions, ensuring their closed shell nature and the occurrence of attractive forces within the studied homodimers. Symmetry-adapted perturbation theory-based energy decomposition analysis alluded to the dispersion force as the main physical component beyond the occurrence of the examined interactions. The obtained findings would be considered as a fundamental underpinning for forthcoming studies pertinent to chemistry, materials science, and crystal engineering.
Collapse
Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Sherif M. A. Saad
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Muhammad Naeem Ahmed
- Department
of Chemistry, The University of Azad Jammu
and Kashmir, Muzaffarabad 13100, Pakistan
| | - Ahmed M. Shawky
- Science
and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mahmoud E. S. Soliman
- Molecular
Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Gamal A. H. Mekhemer
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Al-shimaa S. M. Rady
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| |
Collapse
|
8
|
Yeo CI, Tan YS, Kwong HC, Lee VS, Tiekink ERT. I⋯N halogen bonding in 1 : 1 co-crystals formed between 1,4-diiodotetrafluorobenzene and the isomeric n-pyridinealdazines ( n = 2, 3 and 4): assessment of supramolecular association and influence upon solid-state photoluminescence properties. CrystEngComm 2022. [DOI: 10.1039/d2ce01165d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
1 : 1 co-crystals formed between 1,4-diiodotetrafluorobenzene and each of the three isomeric n-pyridinealdazines (n = 2, 3 and 4), featuring I⋯N halogen bonding contacts within one-dimensional chains, are described.
Collapse
Affiliation(s)
- Chien Ing Yeo
- Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Yee Seng Tan
- Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Huey Chong Kwong
- Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | | | - Edward R. T. Tiekink
- Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| |
Collapse
|